[English] 日本語
Yorodumi
- PDB-5uni: Critical role of water molecules for proton translocation of the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uni
TitleCritical role of water molecules for proton translocation of the membrane-bound transhydrogenase
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Transmembrane / proton channel / high resolution
Function / homology
Function and homology information


: / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
BENZAMIDINE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsPadayatti, P.S. / Leung, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM103838-03 United States
CitationJournal: Structure / Year: 2017
Title: Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase.
Authors: Padayatti, P.S. / Leung, J.H. / Mahinthichaichan, P. / Tajkhorshid, E. / Ishchenko, A. / Cherezov, V. / Soltis, S.M. / Jackson, J.B. / Stout, C.D. / Gennis, R.B. / Zhang, Q.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,21818
Polymers37,4492
Non-polymers2,76916
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-82 kcal/mol
Surface area15430 Å2
MethodPISA
2
A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
hetero molecules

A: NAD(P) transhydrogenase subunit alpha 2
B: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,43736
Polymers74,8984
Non-polymers5,53932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area26770 Å2
ΔGint-186 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.858, 108.936, 109.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
NAD(P) transhydrogenase subunit ... , 2 types, 2 molecules AB

#1: Protein NAD(P) transhydrogenase subunit alpha 2


Mass: 10168.106 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1779 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72GR9, EC: 1.6.1.2
#2: Protein NAD(P) transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta / Tranhydrogenase chain B


Mass: 27280.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1778 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GS0, EC: 1.6.1.2

-
Non-polymers , 5 types, 65 molecules

#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.54 % / Description: Thin needles of 10 x 3 x 1 um
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 1:1 60 mg/mL protein / 1-(8Z-pentadecenoyl)-rac-glycerol (mixed using a mechanical syringe mixer) in MAG 8.7 and precipitant (30% PEG400, 0.1 M MES, pH 6.5, 0.1-0.4 M magnesium nitrate, 1.0- ...Details: 1:1 60 mg/mL protein / 1-(8Z-pentadecenoyl)-rac-glycerol (mixed using a mechanical syringe mixer) in MAG 8.7 and precipitant (30% PEG400, 0.1 M MES, pH 6.5, 0.1-0.4 M magnesium nitrate, 1.0-2.5% benzamidine hydrochloride)
PH range: 6.5-6.8

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.2→43.34 Å / Num. obs: 24963 / % possible obs: 96 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.28 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.2→43.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.115 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22343 1311 5.3 %RANDOM
Rwork0.18637 ---
obs0.18831 23658 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 159 49 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192828
X-RAY DIFFRACTIONr_bond_other_d0.0020.022920
X-RAY DIFFRACTIONr_angle_refined_deg1.9582.0013796
X-RAY DIFFRACTIONr_angle_other_deg1.07636659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89322.26775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.215158
X-RAY DIFFRACTIONr_chiral_restr0.120.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02647
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9354.0691423
X-RAY DIFFRACTIONr_mcbond_other3.934.0671422
X-RAY DIFFRACTIONr_mcangle_it5.6956.0761777
X-RAY DIFFRACTIONr_mcangle_other5.6966.0781778
X-RAY DIFFRACTIONr_scbond_it5.6265.1021405
X-RAY DIFFRACTIONr_scbond_other5.6245.1031406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1977.3052020
X-RAY DIFFRACTIONr_long_range_B_refined13.41735.5013172
X-RAY DIFFRACTIONr_long_range_B_other13.42535.313168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 88 -
Rwork0.277 1747 -
obs--97.14 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more